class PlateViewer(wx.Frame, CPATool): def __init__(self, parent, size=(800,-1), **kwargs): wx.Frame.__init__(self, parent, -1, size=size, title='Plate Viewer', **kwargs) CPATool.__init__(self) self.SetName(self.tool_name) self.SetBackgroundColour("white") # Fixing the color # Check for required properties fields. fail = False for field in required_fields: if not p.field_defined(field): fail = True raise Exception('Properties field "%s" is required for PlateViewer.'%(field)) if fail: self.Destroy() return self.chMap = p.image_channel_colors[:] self.menuBar = wx.MenuBar() self.SetMenuBar(self.menuBar) self.fileMenu = wx.Menu() self.exitMenuItem = self.fileMenu.Append(id=wx.ID_EXIT, text='Exit\tCtrl+Q', help='Close Plate Viewer') self.GetMenuBar().Append(self.fileMenu, 'File') self.menuBar.Append(cpa.helpmenu.make_help_menu(self), 'Help') save_csv_menu_item = self.fileMenu.Append(-1, 'Save table to CSV\tCtrl+S') self.Bind(wx.EVT_MENU, self.on_save_csv, save_csv_menu_item) wx.EVT_MENU(self, wx.ID_EXIT, lambda _:self.Close()) dataSourceSizer = wx.StaticBoxSizer(wx.StaticBox(self, label='Source:'), wx.VERTICAL) dataSourceSizer.Add(wx.StaticText(self, label='Data source:')) self.sourceChoice = TableComboBox(self, -1, size=fixed_width) dataSourceSizer.Add(self.sourceChoice) dataSourceSizer.AddSpacer((-1,3)) dataSourceSizer.Add(wx.StaticText(self, label='Measurement:')) measurements = get_non_blob_types_from_table(p.image_table) self.measurementsChoice = ComboBox(self, choices=measurements, size=fixed_width) self.measurementsChoice.Select(0) dataSourceSizer.Add(self.measurementsChoice) dataSourceSizer.Add(wx.StaticText(self, label='Filter:')) self.filterChoice = FilterComboBox(self, size=fixed_width) dataSourceSizer.Add(self.filterChoice) groupingSizer = wx.StaticBoxSizer(wx.StaticBox(self, label='Data aggregation:'), wx.VERTICAL) groupingSizer.Add(wx.StaticText(self, label='Aggregation method:')) aggregation = ['mean', 'sum', 'median', 'stdev', 'cv%', 'min', 'max'] self.aggregationMethodsChoice = ComboBox(self, choices=aggregation, size=fixed_width) self.aggregationMethodsChoice.Select(0) groupingSizer.Add(self.aggregationMethodsChoice) viewSizer = wx.StaticBoxSizer(wx.StaticBox(self, label='View options:'), wx.VERTICAL) viewSizer.Add(wx.StaticText(self, label='Color map:')) maps = [m for m in matplotlib.cm.datad.keys() if not m.endswith("_r")] maps.sort() self.colorMapsChoice = ComboBox(self, choices=maps, size=fixed_width) self.colorMapsChoice.SetSelection(maps.index('jet')) viewSizer.Add(self.colorMapsChoice) viewSizer.AddSpacer((-1,3)) viewSizer.Add(wx.StaticText(self, label='Well display:')) if p.image_thumbnail_cols: choices = pmp.all_well_shapes else: choices = list(pmp.all_well_shapes) choices.remove(pmp.THUMBNAIL) self.wellDisplayChoice = ComboBox(self, choices=choices, size=fixed_width) self.wellDisplayChoice.Select(0) viewSizer.Add(self.wellDisplayChoice) viewSizer.AddSpacer((-1,3)) viewSizer.Add(wx.StaticText(self, label='Number of plates:')) self.numberOfPlatesTE = wx.TextCtrl(self, -1, '1', style=wx.TE_PROCESS_ENTER) viewSizer.Add(self.numberOfPlatesTE) if not p.plate_id: self.numberOfPlatesTE.Disable() annotationSizer = wx.StaticBoxSizer(wx.StaticBox(self, label='Annotation:'), wx.VERTICAL) annotationSizer.Add(wx.StaticText(self, label='Annotation column:')) annotationColSizer = wx.BoxSizer(wx.HORIZONTAL) self.annotation_cols = dict([(col, db.GetColumnType(p.image_table, col)) for col in db.GetUserColumnNames(p.image_table)]) self.annotationCol = ComboBox(self, choices=self.annotation_cols.keys(), size=(120,-1)) if len(self.annotation_cols) > 0: self.annotationCol.SetSelection(0) annotationColSizer.Add(self.annotationCol, flag=wx.ALIGN_CENTER_VERTICAL) annotationColSizer.AddSpacer((3,-1)) self.addAnnotationColBtn = wx.Button(self, -1, 'Add', size=(44,-1)) annotationColSizer.Add(self.addAnnotationColBtn, flag=wx.ALIGN_CENTER_VERTICAL) annotationSizer.Add(annotationColSizer) annotationSizer.AddSpacer((-1,3)) annotationSizer.Add(wx.StaticText(self, label='Label:')) self.annotationLabel = wx.TextCtrl(self, -1, 'Select wells')#, style=wx.TE_PROCESS_ENTER) self.annotationLabel.Disable() self.annotationLabel.SetForegroundColour(wx.Colour(80,80,80)) self.annotationLabel.SetBackgroundColour(wx.LIGHT_GREY) annotationSizer.Add(self.annotationLabel) annotationSizer.AddSpacer((-1,3)) self.outlineMarked = wx.CheckBox(self, -1, label='Outline annotated wells') annotationSizer.Add(self.outlineMarked) annotationSizer.AddSpacer((-1,3)) self.annotationShowVals = wx.CheckBox(self, -1, label='Show values on plate') annotationSizer.Add(self.annotationShowVals) if len(db.GetUserColumnNames(p.image_table)) == 0: self.outlineMarked.Disable() self.annotationShowVals.Disable() controlSizer = wx.BoxSizer(wx.VERTICAL) controlSizer.Add(dataSourceSizer, 0, wx.EXPAND) controlSizer.AddSpacer((-1,3)) controlSizer.Add(groupingSizer, 0, wx.EXPAND) controlSizer.AddSpacer((-1,3)) controlSizer.Add(viewSizer, 0, wx.EXPAND) controlSizer.AddSpacer((-1,3)) controlSizer.Add(annotationSizer, 0 , wx.EXPAND) self.plateMapSizer = wx.GridSizer(1,1,5,5) self.plateMaps = [] self.plateMapChoices = [] self.rightSizer = wx.BoxSizer(wx.VERTICAL) self.rightSizer.Add(self.plateMapSizer, 1, wx.EXPAND|wx.BOTTOM, 10) self.colorBar = ColorBarPanel(self, 'jet', size=(-1,25)) self.rightSizer.Add(self.colorBar, 0, wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL) mainSizer = wx.BoxSizer(wx.HORIZONTAL) mainSizer.Add(controlSizer, 0, wx.LEFT|wx.TOP|wx.BOTTOM, 10) mainSizer.Add(self.rightSizer, 1, wx.EXPAND|wx.ALL, 10) self.SetSizer(mainSizer) self.SetClientSize((self.Size[0],self.Sizer.CalcMin()[1])) self.sourceChoice.Bind(wx.EVT_COMBOBOX, self.UpdateMeasurementChoice) self.measurementsChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectMeasurement) self.measurementsChoice.Select(0) self.aggregationMethodsChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectAggregationMethod) self.colorMapsChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectColorMap) self.numberOfPlatesTE.Bind(wx.EVT_TEXT_ENTER, self.OnEnterNumberOfPlates) self.wellDisplayChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectWellDisplay) self.annotationCol.Bind(wx.EVT_COMBOBOX, self.OnSelectAnnotationCol) self.addAnnotationColBtn.Bind(wx.EVT_BUTTON, self.OnAddAnnotationCol) self.annotationLabel.Bind(wx.EVT_KEY_UP, self.OnEnterAnnotation) self.outlineMarked.Bind(wx.EVT_CHECKBOX, self.OnOutlineMarked) self.annotationShowVals.Bind(wx.EVT_CHECKBOX, self.OnShowAnnotationValues) self.filterChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectFilter) self.AddPlateMap() self.OnSelectMeasurement() def AddPlateMap(self, plateIndex=0): ''' Adds a new blank plateMap to the PlateMapSizer. ''' data = np.ones(p.plate_shape) # Try to get explicit labels for all wells. res = db.execute('SELECT DISTINCT %s FROM %s WHERE %s != "" and %s IS NOT NULL'% (dbconnect.UniqueWellClause(), p.image_table, p.well_id, p.well_id)) if p.plate_id: self.plateMapChoices += [ComboBox(self, choices=db.GetPlateNames(), size=(400,-1))] self.plateMapChoices[-1].Select(plateIndex) self.plateMapChoices[-1].Bind(wx.EVT_COMBOBOX, self.OnSelectPlate) #plate_col_type = db.GetColumnType(p.image_table, p.plate_id) #plate_id = plate_col_type(self.plateMapChoices[-1].GetString(plateIndex)) plateMapChoiceSizer = wx.BoxSizer(wx.HORIZONTAL) plateMapChoiceSizer.Add(wx.StaticText(self, label='Plate:'), flag=wx.ALIGN_CENTER_VERTICAL) plateMapChoiceSizer.Add(self.plateMapChoices[-1], flag=wx.ALIGN_CENTER_VERTICAL) well_keys = res platemap = pmp.PlateMapPanel(self, data, well_keys, p.plate_shape, colormap = self.colorMapsChoice.Value, well_disp = self.wellDisplayChoice.Value) platemap.add_well_selection_handler(self.OnSelectWell) self.plateMaps += [platemap] singlePlateMapSizer = wx.BoxSizer(wx.VERTICAL) if p.plate_id: singlePlateMapSizer.Add(plateMapChoiceSizer, 0, wx.ALIGN_CENTER) singlePlateMapSizer.Add(platemap, 1, wx.EXPAND|wx.ALIGN_CENTER) self.plateMapSizer.Add(singlePlateMapSizer, 1, wx.EXPAND|wx.ALIGN_CENTER) def UpdatePlateMaps(self): self.measurement = self.measurementsChoice.Value measurement = self.measurement table = self.sourceChoice.Value self.aggMethod = self.aggregationMethodsChoice.Value categorical = measurement not in get_numeric_columns_from_table(table) fltr = self.filterChoice.Value self.colorBar.ClearNotifyWindows() q = sql.QueryBuilder() well_key_cols = [sql.Column(p.image_table, col) for col in well_key_columns()] select = list(well_key_cols) if not categorical: if self.aggMethod=='mean': select += [sql.Column(table, measurement, 'AVG')] elif self.aggMethod=='stdev': select += [sql.Column(table, measurement, 'STDDEV')] elif self.aggMethod=='cv%': # stddev(col) / avg(col) * 100 select += [sql.Expression( sql.Column(table, measurement, 'STDDEV'), ' / ', sql.Column(table, measurement, 'AVG'), ' * 100')] elif self.aggMethod=='sum': select += [sql.Column(table, measurement, 'SUM')] elif self.aggMethod=='min': select += [sql.Column(table, measurement, 'MIN')] elif self.aggMethod=='max': select += [sql.Column(table, measurement, 'MAX')] elif self.aggMethod=='median': select += [sql.Column(table, measurement, 'MEDIAN')] elif self.aggMethod=='none': select += [sql.Column(table, measurement)] else: select += [sql.Column(table, measurement)] q.set_select_clause(select) q.set_group_columns(well_key_cols) if fltr not in (FilterComboBox.NO_FILTER, FilterComboBox.NEW_FILTER, ''): if fltr in p._filters: q.add_filter(p._filters[fltr]) elif fltr in p.gates: q.add_filter(p.gates[fltr].as_filter()) else: raise Exception('Could not find filter "%s" in gates or filters'%(fltr)) wellkeys_and_values = db.execute(str(q)) wellkeys_and_values = np.array(wellkeys_and_values, dtype=object) # Replace measurement None's with nan for row in wellkeys_and_values: if row[-1] is None: row[-1] = np.nan data = [] key_lists = [] dmax = -np.inf dmin = np.inf if p.plate_id: for plateChoice, plateMap in zip(self.plateMapChoices, self.plateMaps): plate = plateChoice.Value plateMap.SetPlate(plate) self.colorBar.AddNotifyWindow(plateMap) self.keys_and_vals = [v for v in wellkeys_and_values if str(v[0])==plate] platedata, wellkeys, ignore = FormatPlateMapData(self.keys_and_vals, categorical) data += [platedata] key_lists += [wellkeys] if not categorical: dmin = np.nanmin([float(kv[-1]) for kv in self.keys_and_vals]+[dmin]) dmax = np.nanmax([float(kv[-1]) for kv in self.keys_and_vals]+[dmax]) else: self.colorBar.AddNotifyWindow(self.plateMaps[0]) platedata, wellkeys, ignore = FormatPlateMapData(wellkeys_and_values, categorical) data += [platedata] key_lists += [wellkeys] if not categorical: dmin = np.nanmin([float(kv[-1]) for kv in wellkeys_and_values]) dmax = np.nanmax([float(kv[-1]) for kv in wellkeys_and_values]) if not categorical: if len(wellkeys_and_values) > 0: # Compute the global extents if there is any data whatsoever gmin = np.nanmin([float(vals[-1]) for vals in wellkeys_and_values]) gmax = np.nanmax([float(vals[-1]) for vals in wellkeys_and_values]) if np.isinf(dmin) or np.isinf(dmax): gmin = gmax = dmin = dmax = 1. # Warn if there was no data for this plate (and no filter was used) if fltr == FilterComboBox.NO_FILTER: wx.MessageBox('No numeric data was found in "%s.%s" for plate "%s"' %(table, measurement, plate), 'Warning') else: gmin = gmax = 1. if fltr == FilterComboBox.NO_FILTER: wx.MessageBox('No numeric data was found in %s.%s' %(table, measurement), 'Warning') if categorical: self.colorBar.Hide() else: self.colorBar.Show() self.colorBar.SetLocalExtents([dmin,dmax]) self.colorBar.SetGlobalExtents([gmin,gmax]) self.rightSizer.Layout() for keys, d, plateMap in zip(key_lists, data, self.plateMaps): plateMap.SetWellKeys(keys) if categorical: plateMap.SetData(np.ones(d.shape) * np.nan) plateMap.SetTextData(d) else: plateMap.SetData(d, data_range=self.colorBar.GetLocalExtents(), clip_interval=self.colorBar.GetLocalInterval(), clip_mode=self.colorBar.GetClipMode()) for keys, d, plateMap in zip(key_lists, data, self.plateMaps): plateMap.SetWellKeys(keys) if categorical: plateMap.SetData(np.ones(d.shape) * np.nan) plateMap.SetTextData(d) else: plateMap.SetData(d, data_range=self.colorBar.GetLocalExtents(), clip_interval=self.colorBar.GetLocalInterval(), clip_mode=self.colorBar.GetClipMode()) def UpdateMeasurementChoice(self, evt=None): ''' Handles the selection of a source table (per-image or per-object) from a choice box. The measurement choice box is populated with the names of numeric columns from the selected table. ''' table = self.sourceChoice.Value if table == TableComboBox.OTHER_TABLE: t = get_other_table_from_user(self) if t is not None: self.sourceChoice.Items = self.sourceChoice.Items[:-1] + [t] + self.sourceChoice.Items[-1:] self.sourceChoice.Select(self.sourceChoice.Items.index(t)) table = t else: self.sourceChoice.Select(0) return self.measurementsChoice.SetItems(get_non_blob_types_from_table(table)) self.measurementsChoice.Select(0) self.colorBar.ResetInterval() self.UpdatePlateMaps() def on_save_csv(self, evt): defaultFileName = 'my_plate_table.csv' saveDialog = wx.FileDialog(self, message="Save as:", defaultDir=os.getcwd(), defaultFile=defaultFileName, wildcard='csv|*', style=(wx.SAVE | wx.FD_OVERWRITE_PROMPT | wx.FD_CHANGE_DIR)) if saveDialog.ShowModal() == wx.ID_OK: filename = saveDialog.GetPath() self.save_to_csv(filename) self.Title = filename saveDialog.Destroy() def save_to_csv(self, filename): with open(filename, 'wb') as f: w = csv.writer(f) w.writerow(['Plate', 'Well', self.measurement + ' ' + self.aggMethod]) w.writerows(self.keys_and_vals) logging.info('Table saved to %s'%filename) def OnSelectPlate(self, evt): ''' Handles the selection of a plate from the plate choice box. ''' self.UpdatePlateMaps() def OnSelectMeasurement(self, evt=None): ''' Handles the selection of a measurement to plot from a choice box. ''' selected_measurement = self.measurementsChoice.Value table = self.sourceChoice.Value numeric_measurements = get_numeric_columns_from_table(table) if (selected_measurement in numeric_measurements): self.aggregationMethodsChoice.Enable() self.colorMapsChoice.Enable() else: self.aggregationMethodsChoice.Disable() self.colorMapsChoice.Disable() self.colorBar.ResetInterval() self.UpdatePlateMaps() def OnSelectAggregationMethod(self, evt=None): ''' Handles the selection of an aggregation method from the choice box. ''' self.colorBar.ResetInterval() self.UpdatePlateMaps() def OnSelectColorMap(self, evt=None): ''' Handles the selection of a color map from a choice box. ''' map = self.colorMapsChoice.Value cm = matplotlib.cm.get_cmap(map) self.colorBar.SetMap(map) for plateMap in self.plateMaps: plateMap.SetColorMap(map) def OnSelectWellDisplay(self, evt=None): ''' Handles the selection of a well display choice from a choice box. ''' sel = self.wellDisplayChoice.Value if sel.lower() == 'image': dlg = wx.MessageDialog(self, 'This mode will render each well as a shrunken image loaded ' 'from that well. This feature is currently VERY SLOW since it ' 'requires loading hundreds of full sized images. Are you sure ' 'you want to continue?', 'Load all images?', wx.OK|wx.CANCEL|wx.ICON_QUESTION) if dlg.ShowModal() != wx.ID_OK: self.wellDisplayChoice.SetSelection(0) return if sel.lower() in ['image', 'thumbnail']: self.colorBar.Hide() else: self.colorBar.Show() for platemap in self.plateMaps: platemap.SetWellDisplay(sel) def OnEnterNumberOfPlates(self, evt=None): ''' Handles the entry of a plates to view from a choice box. ''' try: nPlates = int(self.numberOfPlatesTE.GetValue()) except: logging.warn('Invalid # of plates! Please enter a number between 1 and 100') return if nPlates>100: logging.warn('Too many plates! Please enter a number between 1 and 100') return if nPlates<1: logging.warn('You must display at least 1 plate.') self.numberOfPlatesTE.SetValue('1') nPlates = 1 # Record the indices of the plates currently selected. # Pad the list with sequential plate indices then crop to the new number of plates. currentPlates = [plateChoice.GetSelection() for plateChoice in self.plateMapChoices] currentPlates = (currentPlates+[(currentPlates[-1]+1+p) % len(db.GetPlateNames()) for p in range(nPlates)])[:nPlates] # Remove all plateMaps self.plateMapSizer.Clear(deleteWindows=True) self.plateMaps = [] self.plateMapChoices = [] # Restructure the plateMapSizer appropriately rows = cols = np.ceil(np.sqrt(nPlates)) self.plateMapSizer.SetRows(rows) self.plateMapSizer.SetCols(cols) # Add the plate maps for plateIndex in currentPlates: self.AddPlateMap(plateIndex) self.UpdatePlateMaps() self.plateMapSizer.Layout() # Update outlines self.OnOutlineMarked() def OnSelectWell(self): '''When wells are selected: display their annotation in the annotation label control. If multiple annotations are found then make sure the user knows. ''' wellkeys = [] for pm in self.plateMaps: wellkeys += pm.get_selected_well_keys() if len(wellkeys) > 0 and self.annotationCol.Value != '': self.annotationLabel.Enable() self.annotationLabel.SetForegroundColour(wx.BLACK) self.annotationLabel.SetBackgroundColour(wx.WHITE) annotations = db.execute('SELECT %s FROM %s WHERE %s'%( self.annotationCol.Value, p.image_table, GetWhereClauseForWells(wellkeys))) annotations = list(set([a[0] for a in annotations])) if len(annotations) == 1: if annotations[0] == None: self.annotationLabel.SetValue('') else: self.annotationLabel.SetValue(str(annotations[0])) else: self.annotationLabel.SetValue(','.join([str(a) for a in annotations if a is not None])) else: self.annotationLabel.Disable() self.annotationLabel.SetForegroundColour(wx.Colour(80,80,80)) self.annotationLabel.SetBackgroundColour(wx.LIGHT_GREY) self.annotationLabel.SetValue('Select wells') def OnAddAnnotationCol(self, evt): '''Add a new user annotation column to the database. ''' dlg = wx.TextEntryDialog(self, 'New annotation column name: User_','Add Annotation Column') if dlg.ShowModal() != wx.ID_OK: return new_column = 'User_'+dlg.GetValue() # user-type ==> (sql-type, python-type) coltypes = {'Text' : ('VARCHAR(255)', str), 'Number' : ('FLOAT', float)} dlg = wx.SingleChoiceDialog(self, 'What type of annotation column would you like to add?\nThis can not be changed.', 'Add Annotation Column', coltypes.keys(), wx.CHOICEDLG_STYLE) if dlg.ShowModal() != wx.ID_OK: return usertype = dlg.GetStringSelection() db.AppendColumn(p.image_table, new_column, coltypes[usertype][0]) self.annotation_cols[new_column] = coltypes[usertype][1] self.annotationCol.Items += [new_column] self.annotationCol.SetSelection(len(self.annotation_cols) - 1) current_selection = self.measurementsChoice.Selection self.measurementsChoice.SetItems(self.measurementsChoice.Strings + [new_column]) if self.annotationShowVals.IsChecked(): column = self.annotationCol.Value self.sourceChoice.SetStringSelection(p.image_table) self.measurementsChoice.SetStringSelection(column) self.UpdatePlateMaps() else: self.measurementsChoice.SetSelection(current_selection[0]) self.annotationShowVals.Enable() self.outlineMarked.Enable() self.OnSelectWell() def OnSelectAnnotationCol(self, evt=None): '''Handles selection of an annotation column. ''' col = self.annotationCol.Value if col == '': return coltype = self.annotation_cols[col] self.OnSelectWell() self.OnOutlineMarked() if self.annotationShowVals.IsChecked(): if coltype != str: self.colorMapsChoice.Enable() else: self.colorMapsChoice.Disable() self.measurementsChoice.SetStringSelection(col) self.UpdatePlateMaps() def OnEnterAnnotation(self, evt=None): '''Store the annotation value in the annotation column of the db. ''' if evt.KeyCode < 32 or evt.KeyCode > 127: return column = self.annotationCol.Value value = self.annotationLabel.Value wellkeys = [] for pm in self.plateMaps: wellkeys += pm.get_selected_well_keys() if value == '': value = None elif self.annotation_cols[column] == float: try: value = float(value) self.annotationLabel.SetForegroundColour(wx.BLACK) except: self.annotationLabel.SetForegroundColour(wx.Color(255,0,0)) return db.UpdateWells(p.image_table, column, value, wellkeys) if self.outlineMarked.IsChecked(): for pm in self.plateMaps: if value is None: pm.UnOutlineWells(wellkeys) else: pm.OutlineWells(wellkeys) if (self.sourceChoice.Value == p.image_table and self.measurementsChoice.Value == column): self.UpdatePlateMaps() def OnOutlineMarked(self, evt=None): '''Outlines all non-NULL values of the current annotation ''' # Disable filters when outlining marked wells #if self.outlineMarked.IsChecked(): #self.filterChoice.SetStringSelection(FilterComboBox.NO_FILTER) #self.filterChoice.Disable() #else: #if not self.annotationShowVals.IsChecked(): #self.filterChoice.Enable() # Update outlined wells in PlateMapPanels for pm in self.plateMaps: if self.outlineMarked.IsChecked(): column = self.annotationCol.Value if p.plate_id: res = db.execute('SELECT %s, %s FROM %s WHERE %s="%s"'%( dbconnect.UniqueWellClause(), column, p.image_table, p.plate_id, pm.plate)) else: # if there's no plate_id, we assume there is only 1 plate # and fetch all the data res = db.execute('SELECT %s, %s FROM %s'%( dbconnect.UniqueWellClause(), column, p.image_table)) keys = [tuple(r[:-1]) for r in res if r[-1] is not None] pm.SetOutlinedWells(keys) else: pm.SetOutlinedWells([]) self.UpdatePlateMaps() def OnShowAnnotationValues(self, evt=None): '''Handler for the show values checkbox. ''' if self.annotationShowVals.IsChecked(): column = self.annotationCol.Value self.sourceChoice.SetStringSelection(p.image_table) self.measurementsChoice.SetItems(get_non_blob_types_from_table(p.image_table)) self.measurementsChoice.SetStringSelection(column) self.filterChoice.SetStringSelection(FilterComboBox.NO_FILTER) self.sourceChoice.Disable() self.measurementsChoice.Disable() self.filterChoice.Disable() self.aggregationMethodsChoice.Disable() self.aggregationMethodsChoice.SetValue('none') else: self.sourceChoice.Enable() self.measurementsChoice.Enable() if not self.outlineMarked.IsChecked(): self.filterChoice.Enable() if db.GetColumnType(self.sourceChoice.Value, self.measurementsChoice.Value) != str: self.aggregationMethodsChoice.Enable() self.aggregationMethodsChoice.SetSelection(0) self.UpdatePlateMaps() def OnSelectFilter(self, evt): self.filterChoice.on_select(evt) self.UpdatePlateMaps() self.colorBar.ResetInterval() def save_settings(self): '''save_settings is called when saving a workspace to file. returns a dictionary mapping setting names to values encoded as strings ''' settings = {'table' : self.sourceChoice.Value, 'measurement' : self.measurementsChoice.Value, 'aggregation' : self.aggregationMethodsChoice.Value, 'colormap' : self.colorMapsChoice.Value, 'well display' : self.wellDisplayChoice.Value, 'number of plates' : self.numberOfPlatesTE.GetValue(), } for i, choice in enumerate(self.plateMapChoices): settings['plate %d'%(i+1)] = choice.Value return settings def load_settings(self, settings): '''load_settings is called when loading a workspace from file. settings - a dictionary mapping setting names to values encoded as strings. ''' if 'table' in settings: self.sourceChoice.SetStringSelection(settings['table']) self.UpdateMeasurementChoice() if 'measurement' in settings: self.measurementsChoice.SetStringSelection(settings['measurement']) self.OnSelectMeasurement() if 'aggregation' in settings: self.aggregationMethodsChoice.SetStringSelection(settings['aggregation']) self.OnSelectAggregationMethod() if 'colormap' in settings: self.colorMapsChoice.SetStringSelection(settings['colormap']) self.OnSelectColorMap() if 'number of plates' in settings: self.numberOfPlatesTE.SetValue(settings['number of plates']) self.OnEnterNumberOfPlates() for s, v in settings.items(): if s.startswith('plate '): self.plateMapChoices[int(s.strip('plate ')) - 1].SetValue(v) # set well display last since each step currently causes a redraw and # this could take a long time if they are displaying images if 'well display' in settings: self.wellDisplayChoice.SetStringSelection(settings['well display']) self.OnSelectWellDisplay()
class ColumnFilterPanel(wx.Panel): ''' Creates a UI that allows the user to create WHERE clauses by selecting 1) a DB column name, 2) a comparator, and 3) a value ''' def __init__(self, parent, tables, allow_delete=True, expression=None, **kwargs): wx.Panel.__init__(self, parent, **kwargs) self.fieldSets = [] self.tables = tables self.types = {} self.types[p.image_table] = db.GetColumnTypes(p.image_table) self.tableChoice = ComboBox(self, choices=self.tables, size=(150, -1), style=wx.CB_READONLY) self.tableChoice.Select(0) self.colChoice = ComboBox(self, choices=db.GetColumnNames(p.image_table), size=(150, -1), style=wx.CB_READONLY) self.colChoice.Select(0) self.comparatorChoice = ComboBox(self, size=(80, -1)) self.update_comparator_choice() self.valueField = wx.ComboBox(self, -1, value='') if allow_delete: self.x_btn = wx.Button(self, -1, 'x', size=(30, -1)) ## if expression is not None: ## self.set_expression(expression) colSizer = wx.BoxSizer(wx.HORIZONTAL) colSizer.Add(self.tableChoice, 1, wx.EXPAND) colSizer.AddSpacer((5, -1)) colSizer.Add(self.colChoice, 1, wx.EXPAND) colSizer.AddSpacer((5, -1)) colSizer.Add(self.comparatorChoice, 0.5, wx.EXPAND) colSizer.AddSpacer((5, -1)) colSizer.Add(self.valueField, 1, wx.EXPAND) if allow_delete: colSizer.AddSpacer((5, -1)) colSizer.Add(self.x_btn, 0, wx.EXPAND) self.SetSizer(colSizer) self.tableChoice.Bind(wx.EVT_COMBOBOX, self.on_select_table) self.colChoice.Bind(wx.EVT_COMBOBOX, self.on_select_col) if allow_delete: self.x_btn.Bind(wx.EVT_BUTTON, self.on_remove) self.Fit() def on_remove(self, evt): self.GrandParent.remove(self) def on_select_col(self, evt): self.update_comparator_choice() self.update_value_choice() def on_select_table(self, evt): self.update_col_choice() self.update_comparator_choice() self.update_value_choice() def update_col_choice(self): table = self.tableChoice.Value self.colChoice.SetItems(db.GetColumnNames(table)) self.colChoice.Select(0) def _get_col_type(self): table = self.tableChoice.Value colidx = self.colChoice.GetSelection() return db.GetColumnTypes(table)[colidx] def update_comparator_choice(self): coltype = self._get_col_type() comparators = [] if coltype in [str, unicode]: comparators = ['=', '!=', 'REGEXP', 'IS', 'IS NOT'] if coltype in [int, float, long]: comparators = ['=', '!=', '<', '>', '<=', '>=', 'IS', 'IS NOT'] self.comparatorChoice.SetItems(comparators) self.comparatorChoice.Select(0) def update_value_choice(self): table = self.tableChoice.Value column = self.colChoice.Value colidx = self.colChoice.GetSelection() coltype = db.GetColumnTypes(table)[colidx] vals = [] # if coltype == str:# or coltype == int or coltype == long: # res = db.execute('SELECT DISTINCT %s FROM %s ORDER BY %s'%(column, table, column)) # vals = [str(row[0]) for row in res] self.valueField.SetItems(vals) def get_filter(self): table = self.tableChoice.Value column = self.colChoice.Value comparator = self.comparatorChoice.GetValue() value = self.valueField.GetValue() if self._get_col_type() in [int, float, long]: # Don't quote numbers return sql.Filter(sql.Column(table, column), comparator, '%s' % (value)) if comparator.upper() in ['IS', 'IS NOT'] and value.upper() == 'NULL': # Don't quote comparisons to NULL return sql.Filter(sql.Column(table, column), comparator, '%s' % (value)) return sql.Filter(sql.Column(table, column), comparator, '"%s"' % (value))